Reversible current gel electrophoresis device for separating biological macromolecules

ABSTRACT

Cassette bodies for use with electrophoresis apparatus can be formed of a single piece of molded or machined plastic. Such cassette bodies can include a plurality of channels that pass through the cassette body, from a proximal end to a distal end. Such channels can be defined by upper and lower chambers. The upper chambers can be in fluid communication with a first buffer pool through a semi-permeable membrane, and the lower chambers can be in fluid communication with a second buffer pool. An electric current can be passed through the first and second buffer pools, and then reversed, to perform an electrophoresis operation that can separate a biomolecule of interest from free probes, and provide for convenient collection of said biomolecule of interest.

CROSS REFERENCE TO RELATED APPLICATIONS

This is the U.S. National Stage of International Application No.PCT/US2010/047563, filed Sep. 1, 2010, which was published in Englishunder PCT Article 21(2), which in turn claims the benefit of U.S.Provisional Patent Application No. 61/239,017, entitled “ReversibleCurrent Gel Electrophoresis Device for Separating BiologicalMacromolecules,” filed Sep. 1, 2009, the disclosure of which isincorporated herein by reference in its entirety.

FIELD

This disclosure concerns a device for the electrophoretic purificationof biological macromolecules and methods of using such devices.

BACKGROUND

Electrophoresis is a method used to separate and analyze biologicalmacromolecules, including proteins, DNA, RNA, and complexes of thesemolecules. Numerous electrophoretic techniques have been developedincluding capillary electrophoresis, gel electrophoresis, paperelectrophoresis, and immunoelectrophoresis.

A common electrophoretic method is gel electrophoresis. In gelelectrophoresis, a gel is formed using compounds such as agarose orpolyacrylamide. A mixture containing the desired compound(s) is placed(or loaded) onto one end of the gel, and the gel is then placed contactwith a liquid buffer. This liquid buffer contains salts, which, whendissolved, form ions within the buffer.

Biological molecules are typically charged, for example when contactedwith electrophoresis buffer. For example, DNA is negatively charged incommon electrophoresis buffers due to the phosphate groups in itsbackbone. Therefore, when electric current is applied to the ends of thegel, the biological molecules move through the gel from one end to theother. Depending on their size, shape, and charge, some molecules movethrough the gel faster than others. As the mixture moves through thegel, molecules of one size, shape, or charge are separated from those ofa different size, shape, and/or charge. The speed at which the moleculespass through the gel and the separation between the various types ofmolecules also depends on the concentration and type of the gel. Ingeneral, molecules pass through thicker gels slower than they do throughthinner gels, though thicker gels typically provide better separation.

The gels can be run horizontally and/or vertically. When runhorizontally, the gel is generally submerged in the buffer. The samplemixture is loaded at one end and run to the other end. When the gel isrun vertically, the sample mixture is loaded at the top of the gel andrun towards the bottom. A vertical gel is generally not submerged inbuffer. Rather it is run on an electrophoresis apparatus that contains abuffer chamber at the top and the bottom of the gel.

Conventional electrophoresis apparatus include cassettes that aretypically two parallel glass plates held apart by spacers. Separation ofbiomolecules within an electrophoresis gel is easily achieved; however,subsequent collection of the isolated molecules for further analysis canbe inefficient and difficult. This is especially true when theindividual biomolecules or complexes containing the biomolecules havedifferent physical characteristics, such as molecular weights and/orcharges. For example, in traditional gel electrophoresis, as a mixtureof biomolecules moves through the gel, molecules of one size, shape, orcharge are separated from those of a different size, shape, and/orcharge. Thus, biomolecules of interest can be spread apart within thecross-linked gel, leaving them not easily accessible. There thus remainsa need for improved electrophoresis apparatus that addresses these andother issues.

SUMMARY

To overcome the problems with conventional gel electrophoreticseparation and purification devices, devices for separating biomoleculesof interest in a complex from free biomolecules and methods of usingthose devices are disclosed herein. While the devices are described withreference to the separation of complexes of biomolecules of interest, itwill be appreciated by those of ordinary skill in the art that any groupof large molecules can be separated from a set of smaller molecules bythe disclosed methods and devices.

One embodiment of a cassette for use with an electrophoresis devicecomprises

a proximal end and a distal end opposite the proximal end, a front faceand a back face substantially parallel to the front face, and at leastone chamber defined between the front face and the back face, thechamber having an upper portion and a lower portion, wherein the upperportion includes an upper opening at or near the proximal end of thecassette and the lower portion includes a lower opening at or near thedistal end of the cassette, and wherein the front face comprises atleast one window opening into the upper portion of the chamber.

In some embodiments, the cassette can further comprise a semi-permeablemembrane covering at least a portion of the at least one window opening.The semi-permeable membrane can be removably secured to the front faceof the cassette. The semi-permeable membrane can be configured to allowpassage of a buffer solution surrounding at least a portion of thecassette, and to at least partially block passage of a biomoleculecontained within the upper portion of the at least one chamber. In someembodiments, a semi-permeable membrane can substantially block passageof a biomolecule of interest, thus substantially preventing it fromexiting the chamber through the window opening.

Some embodiments of a cassette according to the present disclosurecomprise acrylic. Some embodiments of a cassette comprise a unitarybody. Cassettes according to the present disclosure can be integratedwith one or more other components to form an electrophoresis device.

One embodiment of an electrophoresis device comprises a cassette,wherein the cassette comprises a proximal end and a distal end oppositethe proximal end, a front face and a back face substantially parallel tothe front face, and at least one chamber defined between the front faceand the back face, the chamber having an upper portion and a lowerportion, wherein the upper portion includes an upper opening at or nearthe proximal end of the cassette and the lower portion includes a loweropening at or near the distal end of the cassette, and wherein the frontface comprises at least one window opening into the upper portion of thechamber. The electrophoresis device can further comprise a first buffersolution in fluid contact with the lower opening of the lower portion, asecond buffer solution in fluid contact with the window opening of theupper portion, and at least one electrode electrically coupled to eachof the first and second buffer solutions. Fluid contact can include bothdirect and indirect fluid contact. For example, fluid contact caninclude fluid contact through a membrane, such as a semi-permeablemembrane.

In some embodiments of an electrophoresis device, the cassette furthercomprises a semi-permeable membrane covering at least a portion of thewindow opening of the upper portion, such as a membrane comprisingcellulose or cellophane.

Disclosed devices can be used to perform reversible currentelectrophoresis, such that when current is run in a first direction,free molecules elute into the buffer at the distal end of the device.Then the cassette body can be placed into a new bath, the currentreversed, and the biomolecules of interest can then move in the oppositedirection, out of the gel, and back into the buffer solution at theproximal end of the cassette body, where they can then be easilycollected from the device.

For example, one method of separating a biomolecule of interest from asample comprises providing a sample, wherein the sample contains abiomolecule of interest and free probes, loading the sample onto a gelin a lower portion of a cassette body, electrophoresing the sample byapplying a current for a time period sufficient for substantially all ofthe free probes to elute out of a distal end of the lower portion, intoa first buffer solution in a first buffer container, leaving thebiomolecule of interest within the gel, removing the first buffersolution, providing a new buffer solution in fluid contact with thelower portion of the cassette, reversing the current with respect to thegel, and electrophoresing the sample for a time period sufficient forsubstantially all of the biomolecule of interest to elute out of aproximal end of the lower portion, into an upper portion of the cassettebody.

Disclosed methods can further comprise collecting biomolecule ofinterest. Collecting the biomolecule of interest can comprisewithdrawing a volume of buffer solution containing the biomolecule ofinterest from the upper portion of the cassette body. Collecting thebiomolecule of interest can comprise securing a semi-permeable membraneover at least part of the upper portion, so as to prevent substantiallyall of the biomolecule of interest from passing through thesemi-permeable membrane into a second buffer solution in fluid contactwith the upper portion of the cassette.

In some methods, reversing the current with respect to the gel comprisesswitching the polarity of a first and second electrode in electricalcontact with the first and second buffer solutions, respectively. Insome methods, reversing the current with respect to the gel compriseschanging the orientation of the gel with respect to a first and secondelectrode in electrical contact with the first and second buffersolutions, respectively.

Removing the first buffer solution can comprise draining the firstbuffer solution from a buffer container. Providing a new buffer solutionin fluid contact with the lower portion of the cassette can compriserefilling the buffer container with the new buffer solution. In othermethods, removing the first buffer solution comprises removing thecassette from a first buffer container containing the first buffersolution, and providing a new buffer solution in fluid contact with thelower portion of the cassette comprises placing the cassette in a secondbuffer container containing the new buffer solution.

The foregoing and other objects, features, and advantages of theinvention will become more apparent from the following detaileddescription, which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a front elevation view of one embodiment of an electrophoresiscassette body according to the present disclosure.

FIG. 2 is a perspective view of one embodiment of an electrophoresiscassette body.

FIG. 3 is an alternate perspective view of one embodiment of anelectrophoresis cassette body.

FIG. 4 is a cross sectional view taken across line 4-4 in FIG. 2.

FIG. 5 is a perspective view of one embodiment of a comb that can beused with cassette bodies of the present disclosure.

FIG. 6 is a perspective view showing the placement of combs into acassette body.

FIG. 7 is a perspective view of a cassette body having a membrane,according to one embodiment of the present disclosure.

FIG. 8 is a schematic cross sectional view of a cassette body in placewithin a buffer bath.

FIG. 9 is a schematic cross sectional view of the cassette body andbuffer bath of FIG. 8, after current has been applied.

FIG. 10 is a schematic cross sectional view of the cassette body ofFIGS. 8-9, in place in a new buffer bath.

FIG. 11 is a perspective view of an electrode insert.

FIG. 12 is a front elevation view of one embodiment of an electrodeinsert.

FIG. 13 is a block diagram of one method of performing anelectrophoresis gel.

FIG. 14 is a perspective view from the back of another embodiment of anelectrophoresis cassette body according to the present disclosure.

FIG. 15 is a front perspective view of the electrophoresis cassette bodyof FIG. 14.

FIG. 16 is a perspective exploded view of the electrophoresis cassettebody of FIG. 14.

FIG. 17 is a perspective exploded view of the electrophoresis cassettebody of FIG. 15.

FIG. 18 is a cross-section of the electrophoresis cassette body of FIG.14, taken along line 18-18 in FIG. 15.

FIG. 19 is a top view of the electrophoresis cassette body of FIG. 14.

DETAILED DESCRIPTION I. Terms

Unless otherwise noted, technical terms are used according toconventional usage. Definitions of common terms in molecular biology maybe found in Benjamin Lewin, Genes VII, published by Oxford UniversityPress, 2000 (ISBN 019879276X); Kendrew et al. (eds.), The Encyclopediaof Molecular Biology, published by Blackwell Publishers, 1994 (ISBN0632021829); Robert A. Meyers (ed.), Molecular Biology andBiotechnology: a Comprehensive Desk Reference, published by Wiley, John& Sons, Inc., 1995 (ISBN 0471186341); and George P. Rédei, EncyclopedicDictionary of Genomics, Genomics, and Proteomics, 2nd Edition, 2003(ISBN: 0-471-26821-6).

The following explanations of terms and methods are provided to betterdescribe the present disclosure and to guide those of ordinary skill inthe art in the practice of the present disclosure. The singular forms“a,” “an,” and “the” refer to one or more than one, unless the contextclearly dictates otherwise. For example, the term “comprising a probe”includes single or plural probes and is considered equivalent to thephrase “comprising at least one probe.” The term “or” refers to a singleelement of stated alternative elements or a combination of two or moreelements, unless the context clearly indicates otherwise. As usedherein, “comprises” means “includes.” Thus, “comprising A or B,” means“including A, B, or A and B,” without excluding additional elements.

Although methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present disclosure,suitable methods and materials are described below. The materials,methods, and examples are illustrative only and not intended to belimiting.

To facilitate review of the various embodiments of this disclosure, thefollowing explanations of specific terms are provided:

Antibody: A polypeptide ligand that includes at least a light chain orheavy chain immunoglobulin variable region and specifically binds anepitope of an antigen. Antibodies can include monoclonal antibodies,polyclonal antibodies, or fragments of antibodies.

The term “specifically binds” refers to, with respect to an antigen, thepreferential association of an antibody or other ligand, in whole orpart, with a specific polypeptide, such as a specific double-strandedDNA binding protein, for example a transcription factor, such as anactivated transcription factor. A specific binding agent bindssubstantially only to a defined target. It is recognized that a minordegree of non-specific interaction may occur between a molecule, such asa specific binding agent, and a non-target polypeptide. Nevertheless,specific binding can be distinguished as mediated through specificrecognition of the antigen. Although selectively reactive antibodiesbind antigen, they can do so with low affinity. Specific bindingtypically results in greater than 2-fold, such as greater than 5-fold,greater than 10-fold, or greater than 100-fold increase in amount ofbound antibody or other ligand (per unit time) to a target polypeptide,such as compared to a non-target polypeptide. A variety of immunoassayformats are appropriate for selecting antibodies specificallyimmunoreactive with a particular protein. For example, solid-phase ELISAimmunoassays are routinely used to select monoclonal antibodiesspecifically immunoreactive with a protein. See Harlow & Lane,Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, NewYork (1988), for a description of immunoassay formats and conditionsthat can be used to determine specific immunoreactivity.

Antibodies can include a heavy and a light chain, each of which has avariable region, termed the variable heavy (VH) region and the variablelight (VL) region. Together, the VH region and the VL region areresponsible for binding the antigen recognized by the antibody. Thisincludes intact immunoglobulins and the variants and portions of themwell known in the art, such as Fab′ fragments, F(ab)′2 fragments, singlechain Fv proteins (“scFv”), and disulfide stabilized Fv proteins(“dsFv”). A scFv protein is a fusion protein in which a light chainvariable region of an immunoglobulin and a heavy chain variable regionof an immunoglobulin are bound by a linker, while in dsFvs, the chainshave been mutated to introduce a disulfide bond to stabilize theassociation of the chains. The term also includes recombinant forms suchas chimeric antibodies (for example, humanized murine antibodies),heteroconjugate antibodies (such as, bispecific antibodies). See also,Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford,Ill.); Kuby, Immunology, 3rd Ed., W.H. Freeman & Co., New York, 1997.

A “monoclonal antibody” is an antibody produced by a single clone ofB-lymphocytes or by a cell into which the light and heavy chain genes ofa single antibody have been transfected. Monoclonal antibodies areproduced by methods known to those of skill in the art, for instance bymaking hybrid antibody-forming cells from a fusion of myeloma cells withimmune spleen cells. These fused cells and their progeny are termed“hybridomas.” Monoclonal antibodies include humanized monoclonalantibodies.

Aptamer: Small nucleic acid or peptide molecules that bind a specifictarget molecule, such as a target biomolecule or biomolecule ofinterest.

Binding or stable binding: An association between two substances ormolecules, such as the hybridization of one nucleic acid molecule toanother or itself, the association of an antibody with a peptide, or theassociation of a protein with another protein (for example the bindingof a transcription factor to a cofactor) or nucleic acid molecule (forexample the binding of a transcription factor to a partiallydouble-stranded nucleic acid probe).

Binding can be detected by any procedure known to one skilled in theart, such as by physical or functional properties of the molecularcomplex. For example, binding can be detected functionally bydetermining whether binding has an observable effect upon a biosyntheticprocess such as expression of a gene, DNA replication, transcription,translation, and the like.

Physical methods of detecting the binding of complementary strands ofnucleic acid molecules, include but are not limited to, methods such asDNase I or chemical footprinting, gel shift and affinity cleavageassays, Northern blotting, dot blotting and light absorption detectionprocedures. For example, the method can involve detecting a signal, suchas a detectable label, present on one or both nucleic acid molecules (orantibody or protein as appropriate).

The binding between an oligomer and its target nucleic acid can becharacterized by the temperature (T_(m)) at which 50% of the oligomer ismelted from its target. A higher (T_(m)) means a stronger or more stablecomplex relative to a complex with a lower (T_(m)).

Biomolecule: A molecule that can be derived from a living organism, suchas a polypeptide, a carbohydrate, a lipid, a small molecule and thelike. In some examples, with reference to biomolecular polymers, such aspolypeptides and nucleic acids, the sequence of polymer need not befound in nature, but can be produced from monomer building blocks, suchas nucleotides and amino acids. In addition, the monomers need not befound in nature. A biomolecule can be obtained from organisms live ordead, for example nucleic acids polypeptides, carbohydrates, lipids,small molecules and the like isolated from an organism. Biomoleculesalso can be artificially produced molecules, such as recombinantpolypeptides, nucleic acids, carbohydrates, lipids, small molecules andthe like. For example, biomolecules can be produced synthetically orrecombinantly. In some examples, a biomolecule is a nucleic acid, suchas a RNA, DNA or a combination thereof. In some examples, a biomoleculeis a peptide, such as a protein.

Binding site: A region on a protein, nucleic acid (such as DNA, RNA, ora combination thereof) to which other molecules stably bind. In oneexample, a binding site is the site on a DNA molecule, such as apartially double-stranded nucleic acid probe, that a double-stranded DNAbinding protein, such as a transcription factor binds (referred to as atranscription factor binding site).

Buffer solution: An aqueous solution consisting of a mixture of a weakacid and its conjugate base or a weak base and its conjugate acid. Ithas the property that the pH of the solution changes very little when asmall amount of acid or base is added to it. Buffer solutions can keeppH at a nearly constant value in a wide variety of chemicalapplications.

Complementarity and percentage complementarity: A double-stranded DNA orRNA strand includes of two complementary strands of base pairs (or onestrand with a hairpin). Complementary binding occurs when the base ofone nucleic acid molecule forms a hydrogen bond to the base of anothernucleic acid molecule. Normally, the base adenine (A) is complementaryto thymidine (T) and uracil (U), while cytosine (C) is complementary toguanine (G). For example, the sequence 5′-ATCG-3′ of one ssDNA moleculecan bond to 3′-TAGC-5′ of another ssDNA to form a dsDNA. In thisexample, the sequence 5′-ATCG-3′ is the reverse complement of3′-TAGC-5′.

Nucleic acid molecules can be complementary to each other even withoutcomplete hydrogen-bonding of all bases of each molecule. For example,hybridization with a complementary nucleic acid sequence can occur underconditions of differing stringency in which a complement will bind atsome but not all nucleotide positions.

Molecules with complementary nucleic acids form a stable duplex ortriplex when the strands bind, (hybridize), to each other by formingWatson-Crick, Hoogsteen or reverse Hoogsteen base pairs. Stable bindingoccurs when an oligonucleotide molecule remains detectably bound to atarget nucleic acid sequence under the required conditions.

Complementarity is the degree to which bases in one nucleic acid strandbase pair with the bases in a second nucleic acid strand.Complementarity is conveniently described by percentage, that is, theproportion of nucleotides that form base pairs between two strands orwithin a specific region or domain of two strands. For example, if 10nucleotides of a 15-nucleotide oligonucleotide form base pairs with atargeted region of a DNA molecule, that oligonucleotide is said to have66.67% complementarity to the region of DNA targeted.

In the present disclosure, “sufficient complementarity” means that asufficient number of base pairs exist between an oligonucleotidemolecule and a target nucleic acid sequence to achieve detectablebinding. When expressed or measured by percentage of base pairs formed,the percentage complementarity that fulfills this goal can range from aslittle as about 50% complementarity to full (100%) complementary. Ingeneral, sufficient complementarity is at least about 50%, for exampleat least about 75% complementarity, at least about 90% complementarity,at least about 95% complementarity, at least about 98% complementarity,or even at least about 100% complementarity.

A thorough treatment of the qualitative and quantitative considerationsinvolved in establishing binding conditions that allow one skilled inthe art to design appropriate oligonucleotides for use under the desiredconditions is provided by Beltz et al. Methods Enzymol. 100:266-285,1983, and by Sambrook et al. (ed.), Molecular Cloning: A LaboratoryManual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1989.

Contacting: Placement in direct physical association, for example bothin solid form and/or in liquid form (for example the placement of aprobe in contact with a sample or an electrophoresis gel in contact witha solution, such as an electrophoresis buffer). In some examples,contacting can occur in vitro with isolated cells or substantiallycell-free extracts, such as nuclear extracts.

Corresponding: The term “corresponding” is a relative term indicatingsimilarity in position, purpose, or structure. For example, a nucleicacid sequence corresponding to a gene promoter indicates that thenucleic acid sequence is similar to the promoter found in an organism.

Cross-linked polymer: A three-dimensional network formed from thechemical reaction of monomers and a cross-linker.

Double-stranded nucleic acid binding protein: A protein thatspecifically binds to regions of double-stranded nucleic acids, such asduplex DNA, for example the double-stranded region of a partiallydouble-stranded nucleic acid probe. Transcription factors are particularexamples of double-stranded nucleic acid binding proteins, as are sigmafactors in prokaryotic organisms.

Emission or emission signal: The light of a particular wavelengthgenerated from a source. In particular examples, an emission signal isemitted from a fluorophore after the fluorophore absorbs light at itsexcitation wavelengths.

Electromagnetic radiation: A series of electromagnetic waves that arepropagated by simultaneous periodic variations of electric and magneticfield intensity, and that includes radio waves, infrared, visible light,ultraviolet light, X-rays and gamma rays. In particular examples,electromagnetic radiation is emitted by a laser, which can possessproperties of monochromaticity, directionality, coherence, polarization,and intensity. Lasers are capable of emitting light at a particularwavelength (or across a relatively narrow range of wavelengths), forexample such that energy from the laser can excite one fluorophore notanother fluorophore.

Electrophoresis: The process of separating a mixture of chargedmolecules based on the different mobility of these charged molecules inresponse to an applied electric current. A particular type ofelectrophoresis is gel electrophoresis. The mobility of a molecule isgenerally related to the characteristics of the charged molecule, suchas size, shape, and surface charge amongst others. The mobility of amolecule also is influenced by the electrophoretic medium, for examplethe composition of the electrophoresis gel. For example, when theelectrophoretic medium is cross-linked acrylamide (polyacrylamide)increasing the percentage if acrylamide in the gel reduces the size ofthe resulting pores in the gel and retards the mobility of a moleculerelative to a gel with a lower percentage of acrylamide (larger poresize). Gel electrophoresis can be performed for analytical purposes, butcan be used as a preparative technique to partially purify moleculesprior to use of other methods, such as mass spectrometry, PCR, cloning,DNA sequencing, array analysis, and immuno-blotting.

Excitation or excitation signal: The light of a particular wavelengthnecessary and/or sufficient to excite an electron transition to a higherenergy level. In particular examples, an excitation is the light of aparticular wavelength necessary and/or sufficient to excite afluorophore to a state such that the fluorophore will emit a different(such as a longer) wavelength of light then the wavelength of light fromthe excitation signal.

For a period of time sufficient: A phrase used to describe a period oftime in which a desired activity occurs, for example the time it takesfor a biomolecule or a complex of biomolecules (molecular complex orbiomolecular complex) to pass through a portion of an electrophoresisgel under the influence of an applied electric current. For example, thetime it takes for a free biomolecule to travel from a proximal end of agel to the distal end and elute from the distal end of anelectrophoresis gel. In another example, it is the time it takes for amolecular complex, such as a complex containing a biomolecule ofinterest, to pass from a position within an electrophoresis gel to theend of the electrophoresis gel, and elute from that end. It isappreciated by those of ordinary skill in the art that the period oftime sufficient for a free biomolecule to pass from one end of anelectrophoresis gel to the other, or the time it takes for a molecularcomplex, such as a complex containing a biomolecule of interest, to passfrom a position within an electrophoresis gel to the end of theelectrophoresis gel, and elute the end, will depend on such factors asthe composition of the gel, strength of the electric current, and thephysical characteristics of the biomolecules or complexes. It is alsoappreciated that these time periods can be varied by the practitioneraccording to his or her needs.

Hairpin or nucleic acid hairpin: A nucleic acid structure formed from asingle strand of nucleic acid. The strand exhibits self-complementarity,such that the nucleic acid hybridizes with itself, forming a loop at oneend.

Hybridization: The ability of complementary single-stranded DNA or RNAto form a duplex molecule (also referred to as a hybridization complex).Nucleic acid hybridization techniques can be used to form hybridizationcomplexes between a probe, such as the single-stranded portion of apartially double-stranded nucleic acid probe and an indexing probe.

Hybridization conditions resulting in particular degrees of stringencywill vary depending upon the nature of the hybridization method and thecomposition and length of the hybridizing nucleic acid sequences.Generally, the temperature of hybridization and the ionic strength (suchas the Na+ concentration) of the hybridization buffer will determine thestringency of hybridization. Calculations regarding hybridizationconditions for attaining particular degrees of stringency are discussedin Sambrook et al., (1989) Molecular Cloning, second edition, ColdSpring Harbor Laboratory, Plainview, N.Y. (chapters 9 and 11). Thefollowing is an exemplary set of hybridization conditions and is notlimiting:

Very High Stringency (Detects Sequences that Share at Least 90%Identity)

Hybridization: 5×SSC at 65 C for 16 hours

Wash twice: 2×SSC at room temperature (RT) for 15 minutes each

Wash twice: 0.5×SSC at 65 C for 20 minutes each

High Stringency (Detects Sequences that Share at Least 80% Identity)

Hybridization: 5×-6×SSC at 65 C-70 C for 16-20 hours

Wash twice: 2×SSC at RT for 5-20 minutes each

Wash twice: 1×SSC at 55 C-70 C for 30 minutes each

Low Stringency (Detects Sequences that Share at Least 50% Identity)

Hybridization: 6×SSC at RT to 55 C for 16-20 hours

Wash at least twice: 2×-3×SSC at RT to 55 C for 20-30 minutes each.

Isolated: An “isolated” biological component (such as a protein, amolecular complex, a nucleic acid probe, or free biomolecule) has beensubstantially separated or purified away from other biologicalcomponents in the cell of the organism in which the component naturallyoccurs, for example, extra-chromatin DNA and RNA, proteins andorganelles. The term also embraces nucleic acids and proteins preparedby recombinant expression in a host cell as well as chemicallysynthesized nucleic acids. It is understood that the term “isolated”does not imply that the biological component is free of tracecontamination, and can include nucleic acid molecules, proteins ormolecular complexes that are at least 50% isolated, such as at least75%, 80%, 90%, 95%, 98%, 99%, or even 100% isolated.

Label: An agent capable of detection, for example by spectrophotometry,flow cytometry, or microscopy. For example, a label can be attached to aspecific binding agent, such as an antibody or a protein, nucleic acid,and the like, thereby permitting detection of the specific binding agentor a biomolecule bound to the specific binding agent. Specific,non-limiting examples of labels include fluorophores, enzymaticlinkages, and radioactive isotopes and nanoparticles, such assemiconductor nanocrystals. Methods for labeling are discussed forexample in Sambrook et al. (Molecular Cloning: A Laboratory Manual, ColdSpring Harbor, N.Y., 1989) and Ausubel et al. (In Current Protocols inMolecular Biology, John Wiley & Sons, New York, 1998).

Molecular complex: Two or more molecules, such as biomolecules, that arestably bound together, for example a nucleic acid binding protein and anucleic acid molecule, an antibody and an antigen, a ligand and receptorfor the ligand, and the like. In some examples, a molecular complex is atranscription factor bound to a nucleic acid that has a binding site forthe transcription factor.

Mutation: A change of the DNA sequence relative to the native orwild-type sequence, for example in a promoter of a gene. In someinstances, a mutation will alter a characteristic of the DNA sequence,for example the binding of a double-stranded binding protein to the DNAsequence. Mutations include base substitution point mutations,deletions, and insertions as well as combinations thereof. Mutations canbe introduced, for example by molecular biological techniques. In someexamples, a mutation, such as a mutation in the promoter sequence of agene, is introduced during synthesis of an oligonucleotide, such as anoligonucleotide that is part of a partially double-stranded nucleic acidprobe.

Nucleic acid molecule (or sequence): A deoxyribonucleotide orribonucleotide polymer including without limitation, cDNA, mRNA, genomicDNA, and synthetic (such as chemically synthesized) DNA or RNA or acombination of DNA and RNA. The nucleic acid molecule can be doublestranded (ds) or single stranded (ss) or even partially double-stranded.Where single stranded, the nucleic acid molecule can be the sense strandor the antisense strand. Nucleic acid molecules can include naturalnucleotides (such as A, T/U, C, and G), and can also include analogs ofnatural nucleotides. In one embodiment, a nucleic acid molecule is anaptamer.

Nucleotide: The fundamental unit of nucleic acid molecules. A nucleotideincludes a nitrogen-containing base attached to a pentose monosaccharidewith one, two, or three phosphate groups attached by ester linkages tothe saccharide moiety.

The major nucleotides of DNA are deoxyadenosine 5′-triphosphate (dATP orA), deoxyguanosine 5′-triphosphate (dGTP or G), deoxycytidine5′-triphosphate (dCTP or C) and deoxythymidine 5′-triphosphate (dTTP orT). The major nucleotides of RNA are adenosine 5′-triphosphate (ATP orA), guanosine 5′-triphosphate (GTP or G), cytidine 5′-triphosphate (CTPor C) and uridine 5′-triphosphate (UTP or U).

Nucleotides include those nucleotides containing modified bases,modified sugar moieties and modified phosphate backbones, for example asdescribed in U.S. Pat. No. 5,866,336 to Nazarenko et al.

Examples of modified base moieties which can be used to modifynucleotides at any position on its structure include, but are notlimited to: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,hypoxanthine, xanthine, acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N˜6-sopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid,pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil,2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acidmethylester, uracil-5-oxyacetic acid, 5-methyl-2-thiouracil,3-(3-amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.

Examples of modified sugar moieties which may be used to modifynucleotides at any position on its structure include, but are notlimited to: arabinose, 2-fluoroarabinose, xylose, and hexose, or amodified component of the phosphate backbone, such as phosphorothioate,a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, aphosphordiamidate, a methylphosphonate, an alkyl phosphotriester, or aformacetal or analog thereof.

Oligonucleotide or “oligo”: Multiple nucleotides (that is, moleculesincluding a sugar (for example, ribose or deoxyribose) linked to aphosphate group and to an exchangeable organic base, which is either asubstituted pyrimidine (Py) (for example, cytosine (C), thymine (T) oruracil (U)) or a substituted purine (Pu) (for example, adenine (A) orguanine (G)). The term “oligonucleotide” as used herein refers to botholigoribonucleotides and oligodeoxyribonucleotides. Oligonucleotides canbe obtained from existing nucleic acid sources (for example, genomic orcDNA), but are preferably synthetic (that is, produced byoligonucleotide synthesis).

Partially double-stranded nucleic acid probe: A nucleic acid probe thatincludes both a region that is single-stranded and a region or portionthat is double-stranded. A partially double-stranded nucleic acid probehas a portion that is double-stranded and a portion that issingle-stranded, wherein the double-stranded and single-strandedportions are connected, for example covalently linked. In some examples,the double-stranded portion includes a binding site for adouble-stranded nucleic acid binding protein, such as a transcriptionfactor.

Peptide/Protein/Polypeptide: All of these terms refer to a polymer ofamino acids and/or amino acid analogs that are joined by peptide bondsor peptide bond mimetics. The twenty naturally occurring amino acids andtheir single-letter and three-letter designations are known in the art.

Polymerization: The reaction of monomer molecules together in a chemicalreaction to form linear chains or a three-dimensional network of polymerchains. In one embodiment, the polymer polyacrylamide is formed from thepolymerization of acrylamide in the presence of a cross-linker, which insome embodiments is N′,N-methylenebisacrylamide (BIS). Upon theintroduction of catalyst, the polymerization of acrylamide and BISproceeds via a free-radical mechanism. The most common system ofcatalytic initiation involves the production of free oxygen radicals byammonium persulfate (APS) in the presence of the tertiary aliphaticamine N,N,N′,N′-tetramethylethylenediamine (TEMED) although other freeradical generators can be employed.

Polysaccharide: A polymer of covalently linked sugars. The sugars makingup the polysaccharide can by the same sugar or different sugars.

Promoter: An array of nucleic acid control sequences, which directstranscription of a nucleic acid. Typically, a eukaryotic a promoterincludes necessary nucleic acid sequences near the start site oftranscription, such as, in the case of a polymerase II type promoter, aTATA element. A promoter also optionally includes distal enhancer orrepressor elements, which can be located as much as several thousandbase pairs from the start site of transcription, such as specific DNAsequences that are recognized by proteins known as transcriptionfactors.

In prokaryotes, a promoter is recognized by RNA polymerase and anassociated sigma factor, which in turn are brought to the promoter DNAby an activator protein binding to its own DNA sequence nearby.

Reverse: To change direction opposite the initial direction. Forexample, if a biomolecule is traveling away from position A towardposition B, reversing direction would mean that that the biomolecule istraveling away from position B toward position A. Reversing thedirection of travel of a biomolecule in an electrophoresis gel can beaccomplished by reversing the polarity of an electrophoresis apparatus,for example by reversing the direction of the current, while the gelremains static with respect to the electrophoresis apparatus, orreversing the orientation of the gel with respect to the appliedelectric current.

Sample: Any quantity of a substance that includes biomolecules (such asnucleic acid and proteins, for example double-stranded nucleic acidbinding proteins) that can be used in a method disclosed herein. Thesample can be a biological sample or can be extracted from a biologicalsample derived from humans, animals, plants, fungi, yeast, bacteria,tissue cultures, viral cultures, or combinations thereof.

Sequence identity/similarity: The identity/similarity between two ormore nucleic acid sequences, or two or more amino acid sequences, isexpressed in terms of the identity or similarity between the sequences.Sequence identity can be measured in terms of percentage identity; thehigher the percentage, the more identical the sequences are. Homologs ororthologs of nucleic acid or amino acid sequences possess a relativelyhigh degree of sequence identity/similarity when aligned using standardmethods.

Methods of alignment of sequences for comparison are well known in theart. Various programs and alignment algorithms are described in: Smith &Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol.Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp,CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988;Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; andPearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J.Mol. Biol. 215:403-10, 1990, presents a detailed consideration ofsequence alignment methods and homology calculations.

The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J.Mol. Biol. 215:403-10, 1990) is available from several sources,including the National Center for Biological Information (NCBI, NationalLibrary of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894) andon the Internet, for use in connection with the sequence analysisprograms blastp, blastn, blastx, tblastn, and tblastx. Blastn is used tocompare nucleic acid sequences, while blastp is used to compare aminoacid sequences. Additional information can be found at the NCBI website.

Once aligned, the number of matches is determined by counting the numberof positions where an identical nucleotide or amino acid residue ispresented in both sequences. The percent sequence identity is determinedby dividing the number of matches either by the length of the sequenceset forth in the identified sequence, or by an articulated length (suchas 100 consecutive nucleotides or amino acid residues from a sequenceset forth in an identified sequence), followed by multiplying theresulting value by 100. For example, a nucleic acid sequence that has1166 matches when aligned with a test sequence having 1554 nucleotidesis 75.0 percent identical to the test sequence (1166÷1554*100=75.0). Thepercent sequence identity value is rounded to the nearest tenth. Forexample, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The lengthvalue will always be an integer. One indication that two nucleic acidmolecules are closely related is that the two molecules hybridize toeach other under stringent conditions. Stringent conditions aresequence-dependent and are different under different environmentalparameters.

Target biomolecule or biomolecule of interest: A biomolecule about whichinformation is desired. A target biomolecule or biomolecule of interestcan be any molecule that is or once was part of a living organism orsynthetically produced. In several non-limiting examples, a targetbiomolecule is a polypeptide, a nucleic acid, a ligand, or a smallmolecule. In one example, the information desired is location of thebiomolecule on or within a cell, such as a cell in a biological sample.In another example, the information desired is the presence or absenceof the biomolecule, for example in a sample, such as a biologicalsample. In another example, the information desired is the presence,absence, and/or location of the biomolecule in a gel, such as anelectrophoreses gel.

Transcription factor: A protein that regulates transcription. Inparticular, transcription factors regulate the binding of RNA polymeraseand the initiation of transcription. A transcription factor bindsupstream or downstream to either enhance or repress transcription of agene by assisting or blocking RNA polymerase binding. The termtranscription factor includes both inactive and activated transcriptionfactors.

Transcription factors are typically modular proteins that affectregulation of gene expression. Exemplary transcription factors includeAAF, abl, ADA2, ADA-NF1, AF-1, AFP1, AhR, AIIN3, ALL-1, alpha-CBF,alpha-CP1, alpha-CP2a, alpha-CP2b, alphaHo, alphaH2-alphaH3, Alx-4,aMEF-2, AML1, AML1a, AML1b, AML1c, AML1DeltaN, AML2, AML3, AML3a, AML3b,AMY-1L, A-Myb, ANF, AP-1, AP-2alphaA, AP-2alphaB, AP-2beta, AP-2gamma,AP-3 (1), AP-3 (2), AP-4, AP-5, APC, AR, AREB6, Arnt, Arnt (774 M form),ARP-1, ATBF1-A, ATBF1-B, ATF, ATF-1, ATF-2, ATF-3, ATF-3deltaZIP, ATF-a,ATF-adelta, ATPF1, Barhl1, Barhl2, Barx1, Barx2, Bcl-3, BCL-6, BD73,beta-catenin, Bin1, B-Myb, BP1, BP2, brahma, BRCA1, Brn-3a, Brn-3b,Brn-4, BTEB, BTEB2, B-TFIID, C/EBPalpha, C/EBPbeta, C/EBPdelta,CACCbinding factor, Cart-1, CBF (4), CBF (5), CBP, CCAAT-binding factor,CCMT-binding factor, CCF, CCG1, CCK-1a, CCK-1b, CD28RC, cdk2, cdk9,Cdx-1, CDX2, Cdx-4, CFF, Chx1O, CLIM1, CLIM2, CNBP, CoS, COUP, CP1,CP1A, CP1C, CP2, CPBP, CPE binding protein, CREB, CREB-2, CRE-BP1,CRE-BPa, CREMalpha, CRF, Crx, CSBP-1, CTCF, CTF, CTF-1, CTF-2, CTF-3,CTF-5, CTF-7, CUP, CUTL1, Cx, cyclin A, cyclin T1, cyclin T2, cyclinT2a, cyclin T2b, DAP, DAX1, DB1, DBF4, DBP, DbpA, DbpAv, DbpB, DDB,DDB-1, DDB-2, DEF, deltaCREB, deltaMax, DF-1, DF-2, DF-3, Dlx-1, Dlx-2,Dlx-3, DIx4 (long isoform), Dlx-4 (short isoform, Dlx-5, Dlx-6, DP-1,DP-2, DSIF, DSIF-p14, DSIF-p160, DTF, DUX1, DUX2, DUX3, DUX4, E, E12,E2F, E2F+E4, E2F+p107, E2F-1, E2F-2, E2F-3, E2F-4, E2F-5, E2F-6, E47,E4BP4, E4F, E4F1, E4TF2, EAR2, EBP-80, EC2, EF1, EF-C, EGR1, EGR2, EGR3,EIIaE-A, EIIaE-B, EIIaE-Calpha, EIIaE-Cbeta, EivF, EIf-1, Elk-1, Emx-1,Emx-2, Emx-2, En-1, En-2, ENH-bind. prot., ENKTF-1, EPAS1, epsilonF1,ER, Erg-1, Erg-2, ERR1, ERR2, ETF, Ets-1, Ets-1 deltaVi1, Ets-2, Evx-1,F2F, factor 2, Factor name, FBP, f-EBP, FKBP59, FKHL18, FKHRL1P2, Fli-1,Fos, FOXB1, FOXC1, FOXC2, FOXD1, FOXD2, FOXD3, FOXD4, FOXE1, FOXE3,FOXF1, FOXF2, FOXG1a, FOXG1b, FOXG1c, FOXH1, FOXI1, FOXJ1a, FOXJ1b,FOXJ2 (long isoform), FOXJ2 (short isoform), FOXJ3, FOXK1a, FOXK1b,FOXK1c, FOXL1, FOXM1a, FOXM1b, FOXM1c, FOXN1, FOXN2, FOXN3, FOX01a,FOX01b, FOXO2, FOXO3a, FOXO3b, FOXO4, FOXP1, FOXP3, Fra-1, Fra-2, FTF,FTS, G factor, G6 factor, GABP, GABP-alpha, GABP-beta1, GABP-beta2, GADD153, GAF, gammaCMT, gammaCAC1, gammaCAC2, GATA-1, GATA-2, GATA-3,GATA-4, GATA-5, GATA-6, Gbx-1, Gbx-2, GCF, GCMa, GCN5, GF1, GLI, GLI3,GR alpha, GR beta, GRF-1, Gsc, Gscl, GT-IC, GT-IIA, GT-IIBalpha,GT-IIBbeta, H1TF1, H1TF2, H2RIIBP, H4TF-1, H4TF-2, HAND1, HAND2, HB9,HDAC1, HDAC2, HDAC3, hDaxx, heat-induced factor, HEB, HEB1-p67,HEB1-p94, HEF-1 B, HEF-1T, HEF-4C, HEN1, HEN2, Hesx1, Hex, HIF-1,HIF-1alpha, HIF-1beta, HiNF-A, HiNF-B, HINF-C, HINF-D, HiNF-D3, HiNF-E,HiNF-P, HIP1, HIV-EP2, H1f, HLTF, HLTF (Met123), HLX, HMBP, HMG I, HMGI(Y), HMG Y, HMGI-C, HNF-1A, HNF-1B, HNF-1C, HNF-3, HNF-3alpha,HNF-3beta, HNF-3gamma, HNF4, HNF-4-alpha, HNF4alpha1, HNF-4-alpha2,HNF-4-alpha3, HNF-4-alpha4, HNF4gamma, HNF-6alpha, hnRNP K, HOX11,HOXA1, HOXA10, HOXA10 PL2, HOXA11, HOXA13, HOXA2, HOXA3, HOXA4, HOXA5,HOXA6, HOXA7, HOXA9A, HOXA9B, HOXB-1, HOXB13, HOXB2, HOXB3, HOXB4,HOXB5, HOXB6, HOXA5, HOXB7, HOXB8, HOXB9, HOXC10, HOXC11, HOXC12,HOXC13, HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, HOXD10, HOXD11, HOXD12,HOXD13, HOXD3, HOXD4, HOXD8, HOXD9, Hp55, Hp65, HPX42B, HrpF, HSF, HSF1(long), HSF1 (short), HSF2, hsp56, Hsp90, IBP-1, ICER-II, ICER-ligamma,ICSBP, Id1, Id1 H′, Id2, Id3, Id3/Heir-1, IF1, IgPE-1, IgPE-2, IgPE-3,IkappaB, IkappaB-alpha, IkappaB-beta, IkappaBR, II-1 RF, IL-6 RE-BP,II-6 RF, INSAF, IPF1, IRF-1, IRF-2, irlB, 1Rx2a, Irx-3, lrx-4, ISGF-1,ISGF-3, ISGF3alpha, ISGF-3gamma, lsl-1, ITF, ITF-1, ITF-2, JRF, Jun,JunB, JunD, kappay factor, KBP-1, KER1, KER-1, Kox1, KRF-1, Kuautoantigen, KUP, LBP-1, LBP-1a, LBX1, LCR-F1, LEF-1, LEF-1B, LF-A1,LHX1, LHX2, LHX3a, LHX3b, LHX5, LHX6.1a, LHX6.1b, LIT-1, Lmo1, Lmo2,LMX1A, LMX1B, L-My1 (long form), L-My1 (short form), L-My2, LSF,LXRalpha, LyF-1, LyI-1, M factor, Mad1, MASH-1, Max1, Max2, MAZ, MAZ1,MB67, MBF1, MBF2, MBF3, MBP-1 (1), MBP-1 (2), MBP-2, MDBP, MEF-2,MEF-2B, MEF-2C (433 AA form), MEF-2C (465 AA form), MEF-2C (473 M form),MEF-2C/delta32 (441 AA form), MEF-2D00, MEF-2DOB, MEF-2DA0, MEF-2DA′0,MEF-2DAB, MEF-2DA′B, Meis-1, Meis-2a, Meis-2b, Meis-2c, Meis-2d,Meis-2e, Meis3, Meox1, Meox1a, Meox2, MHox (K-2), Mi, MIF-1, Miz-1,MM-1, MOPS, MR, Msx-1, Msx-2, MTB-Zf, MTF-1, mtTF1, Mxi1, Myb, Myc, Myc1, Myf-3, Myf-4, Myf-5, Myf-6, MyoD, MZF-1, NC1, NC2, NCX, NELF, NER1,Net, NF III-a, NF III-c, NF III-e, NF-1, NF-1A, NF-1B, NF-1X, NF-4FA,NF-4FB, NF-4FC, NF-A, NF-AB, NFAT-1, NF-AT3, NF-Atc, NF-Atp, NF-Atx,NfbetaA, NF-CLE0a, NF-CLE0b, NFdeltaE3A, NFdeltaE3B, NFdeltaE3C,NFdeltaE4A, NFdeltaE4B, NFdeltaE4C, Nfe, NF-E, NF-E2, NF-E2 p45, NF-E3,NFE-6, NF-Gma, NF-GMb, NF-IL-2A, NF-IL-2B, NF-jun, NF-kappaB,NF-kappaB(-like), NF-kappaB1, NF-kappaB1, precursor, NF-kappaB2,NF-kappaB2 (p49), NF-kappaB2 precursor, NF-kappaE1, NF-kappaE2,NF-kappaE3, NF-MHCIIA, NF-MHCIIB, NF-muE1, NF-muE2, NF-muE3, NF-S, NF-X,NF-X1, NF-X2, NF-X3, NF-Xc, NF-YA, NF-Zc, NF-Zz, NHP-1, NHP-2, NHP3,NHP4, NKX2-5, NKX2B, NKX2C, NKX2G, NKX3A, NKX3A v1, NKX3A v2, NKX3A v3,NKX3A v4, NKX3B, NKX6A, Nmi, N-Myc, N-Oct-2alpha, N-Oct-2beta, N-Oct-3,N-Oct-4, N-Oct-5a, N-Oct-5b, NP-TCII, NR2E3, NR4A2, Nrf1, Nrf-1, Nrf2,NRF-2beta1, NRF-2gamma1, NRL, NRSF form 1, NRSF form 2, NTF, O2, OCA-B,Oct-1, Oct-2, Oct-2.1, Oct-2B, Oct-2C, Oct-4A, Oct4B, Oct-5, Oct-6,Octa-factor, octamer-binding factor, oct-B2, oct-B3, Otx1, Otx2, OZF,p107, p130, p28 modulator, p300, p38erg, p45, p49erg, -p53, p55, p55erg,p65delta, p67, Pax-1, Pax-2, Pax-3, Pax-3A, Pax-3B, Pax-4, Pax-5, Pax-6,Pax-6/Pd-5a, Pax-7, Pax-8, Pax-8a, Pax-8b, Pax-8c, Pax-8d, Pax-8e,Pax-8f, Pax-9, Pbx-1a, Pbx-1b, Pbx-2, Pbx-3a, Pbx-3b, PC2, PC4, PC5,PEA3, PEBP2alpha, PEBP2beta, Pit-1, PITX1, PITX2, PITX3, PKNOX1, PLZF,PO-B, Pontin52, PPARalpha, PPARbeta, PPARgamma1, PPARgamma2, PPUR, PR,PR A, pRb, PRD1-BF1, PRDI-BFc, Prop-1, PSE1, P-TEFb, PTF, PTFalpha,PTFbeta, PTFdelta, PTFgamma, Pu box binding factor, Pu box bindingfactor (BJA-B), PU.1, PuF, Pur factor, R1, R2, RAR-alpha1, RAR-beta,RAR-beta2, RAR-gamma, RAR-gamma1, RBP60, RBP-Jkappa, Rel, RelA, RelB,RFX, RFX1, RFX2, RFX3, RFX5, RF-Y, RORalpha1, RORalpha2, RORalpha3,RORbeta, RORgamma, Rox, RPF1, RPGalpha, RREB-1, RSRFC4, RSRFC9, RVF,RXR-alpha, RXR-beta, SAP-1a, SAP1b, SF-1, SHOX2a, SHOX2b, SHOXa, SHOXb,SHP, SIII-p110, SIII-p15, SIII-p18, SIM1, Six-1, Six-2, Six-3, Six-4,Six-5, Six-6, SMAD-1, SMAD-2, SMAD-3, SMAD-4, SMAD-5, SOX-11, SOX-12,Sox-4, Sox-5, SOX-9, Sp1, Sp2, Sp3, Sp4, Sph factor, Spi-B, SPIN, SRCAP,SREBP-1a, SREBP-1b, SREBP-1c, SREBP-2, SRE-ZBP, SRF, SRY, SRP1, Staf-50,STAT1alpha, STAT1beta, STAT2, STAT3, STAT4, STAT6, T3R, T3R-alpha1,T3R-alpha2, T3R-beta, TAF(I)110, TAF(I)48, TAF(I)63, TAF(II)100,TAF(II)125, TAF(II)135, TAF(II)170, TAF(II)18, TAF(II)20, TAF(II)250,TAF(II)250Delta, TAF(II)28, TAF(II)30, TAF(II)31, TAF(II)55,TAF(II)70-alpha, TAF(II)70-beta, TAF(II)70-gamma, TAF-I, TAF-II, TAF-L,Tal-1, Tal-1beta, Tal-2, TAR factor, TBP, TBX1A, TBX1 B, TBX2, TBX4,TBX5 (long isoform), TBX5 (short isoform), TCF, TCF-1, TCF-1A, TCF-1B,TCF-1C, TCF-1D, TCF-1E, TCF-1F, TCF-1G, TCF-2alpha, TCF-3, TCF-4,TCF-4(K), TCF-4B, TCF-4E, TCFbeta1, TEF-1, TEF-2, tel, TFE3, TFEB,TFIIA, TFIIA-alpha/beta precursor, TFIIA-alpha/beta precursor,TFIIA-gamma, TFIIB, TFIID, TFIIE, TFIIE-alpha, TFIIE-beta, TFIIF,TFIIF-alpha, TFIIF-beta, TFIIH, TFIIH*, TFIIH-CAK, TFIIH-cyclin H,TFIIH-ERCC2/CAK, TFIIH-MAT1, TFIIH-MO15, TFIIH-p34, TFIIH-p44,TFIIH-p62, TFIIH-p80, TFIIH-p90, TFII-I, Tf-LF1, Tf-LF2, TGIF, TGIF2,TGT3, THRA1, TIF2, TLE1, TLX3, TMF, TR2, TR2-11, TR2-9, TR3, TR4, TRAP,TREB-1, TREB-2, TREB-3, TREF1, TREF2, TRF (2), TTF-1, TXRE BP, TxREF,UBF, UBP-1, UEF-1, UEF-2, UEF-3, UEF-4, USF1, USF2, USF2b, Vav, Vax-2,VDR, vHNF-1A, vHNF-1B, vHNF-1C, VITF, WSTF, WT1, WT1I, WT1 I-KTS, WT1I-del2, WT1-KTS, WT1-del2, X2BP, XBP-1, XW-V, XX, YAF2, YB-1, YEBP, YY1,ZEB, ZF1, ZF2, ZFX, ZHX1, ZIC2, ZID, ZNF174, amongst others.

An activated transcription factor is a transcription factor that hasbeen activated by a stimulus resulting in a measurable change in thestate of the transcription factor, for example a post-translationalmodification, such as phosphorylation, methylation, and the like.Activation of a transcription factor can result in a change in theaffinity for a particular DNA sequence or of a particular protein, suchas another transcription factor and/or cofactor.

Under conditions that permit binding: A phrase used to describe anyenvironment that permits the desired activity, for example conditionsunder which two or more molecules, such as nucleic acid molecules and/orprotein molecules, can bind. Such conditions can include specificconcentrations of salts and/or other chemicals that facilitate thebinding of molecules. In some examples, conditions that permit bindingare similar to the conditions found in the nucleus of a cell, forexample a eukaryotic cell or the cytoplasm of a prokaryotic cell. Suchconditions can be simulated, for example by using a nuclear extract.

Unitary: Having the indivisible character of a unit. For example, aunitary body can comprise a single body, without removable components.

II. Description of Several Embodiments

A. Devices

FIGS. 1-4 illustrate one embodiment of an electrophoresis cassette body100 according to the present disclosure. As shown in FIGS. 8-10 anddescribed in further detail below, cassette body 100 can be used inconjunction with one or more buffer baths in order to perform variousmethods of performing gel electrophoresis.

Returning to FIGS. 1-4, cassette body 100 can include one or more upperchambers 102 adjacent a shelf 106 and one or more lower chambers 104,each in fluid communication with one or more of the upper chambers 102.The terms “upper” and “lower” are used for convenient reference to thefigures and are not meant to be limiting in any way.

Each upper chamber 102 and corresponding lower chamber 104 form arespective channel, or through hole, passing from the shelf 106 at theproximal end 108 of the cassette body 100 to the distal end 110. Eachupper chamber 102 includes an opening 112 at or near the proximal end108 of the cassette body 100, and each lower chamber 104 includes anopening 114 at or near the distal end 110 of the cassette body 100.Upper chambers 102 further include a window 116, which results in aportion of upper chamber 102 being open to the space external tocassette body 100. In some embodiments, cassette body 100 can be amonolithic body such that a front face 132 is formed together with, andnot removable from, a back face 134. Upper and lower chambers 102, 104can be defined between the front face 132 and the back face 134.

Upper chambers 102 and lower chambers 104 can be of substantially thesame size, shape, and/or capacity, or of different sizes, shapes, and/orcapacities. For example, in the embodiments shown in FIGS. 1-3, thelower chambers 104 can be slightly smaller, for example, slightlynarrower, than the upper chambers 102.

Embodiments of cassette bodies can be machined, shaped, or molded toengage with one or more other components to form an electrophoresisapparatus. For example, cassette body 100 can be provided with raisedlips 118 on edge portions 120, 122. Edge portions 120, 122 can beprovided with one or more raised bumps 124 or depressions 126. Someembodiments of cassette bodies can be molded or otherwise formed suchthat a plurality of cassette bodies can be stacked against or on top ofone another. Cassette bodies can be used alone or in conjunction withone or more other cassette bodies in an overall electrophoresis device.

FIG. 5 illustrates a perspective view of a comb 500 that can be usedwith cassette body 100. As shown in FIG. 6, comb 500 can be shaped toengage with cassette body 100. For example, comb 500 can include astopper 502, an elongate portion 504, and a projection 506. The stopper502 can rest within the shelf 106 of the cassette body 100, such that asurface 508 of the comb 500 rests on a surface 510 of the cassette body100. In this configuration, the elongate portion 504 can be positionedwithin the upper chamber 102, and the projection 506 can extend into thelower chamber 104. In the embodiment shown in FIG. 6, the volume, orsize, of the elongate portion 504 is substantially the same as thevolume, or size, of the upper chamber 102. The volume of the projection506 is substantially smaller than the volume of the lower chamber 104,yet the width of the projection 506 and the lower chamber 104 issubstantially the same. Other arrangements, however, are possible. Inalternate embodiments, the elongate portion 504 and the projection 506can be relatively smaller or larger with respect to the upper chamber102 and lower chamber 104, respectively.

The combs 500 can be sized such that the stoppers 502 substantially fillthe volume of the shelf 106 of the cassette body 100. For example, insome embodiments, when the combs 500 are inserted into the upper andlower chambers 102, 104, the stoppers 502 of adjacent combs 500 can besubstantially flush, or at least very near, one another, such that edges512, 514 of neighboring combs contact one another. Comb edges 516, 518can also be in contact with shelf edges 128, 130, respectively, when thecombs 500 are inserted into the upper chambers 102. In alternateembodiments, there can be a space or gap between comb edges 512, 514,and/or between comb edges 516, 518 and shelf edges 128, 130,respectively.

In preparation for running an electrophoresis gel using a cassetteaccording to the present disclosure, such as the cassette body 100 shownin FIGS. 1-4, a compound such as agarose or polyacrylamide can beintroduced into the lower chambers 104. One or more combs, such as acomb 500 shown in FIG. 5, can then be positioned within the upper andlower chambers 102, 104, as shown in FIG. 6, such that the projections506 are positioned within the lower chamber 104, thus displacing avolume of the compound equal to the volume of the projection 504. Oncethe compound becomes a gel, the combs 500 can be removed from thecassette 100. A cross-linked gel can thus be formed in the lowerchambers 104, having an indentation in the upper portion formed byprojection 504, adjacent the upper chamber 102, wherein a sample can beloaded.

Cassette bodies according to the present disclosure can be integratedwith other components, such as membranes and/or electrodes in order tofacilitate providing electrical current to a sample loaded into thechambers of the cassette body.

In some embodiments, as shown in FIG. 7, a membrane 700 can be coupledto a cassette body 702. In some embodiments, a membrane 700 can cover atleast a portion of at least one window 704 provided in an upper chamber706. The membrane 700 also can substantially cover the entire window 704of each upper chamber 706. Alternatively, a separate membrane 700 can beprovided for each window 704. In some embodiments with a plurality ofmembranes 700, each membrane 700 can be substantially the samethickness, and can comprise the same material. In other embodiments witha plurality of membranes 700, one or more membranes 700 can be differentfrom one or more other membranes 700, such as by being a differentthickness and/or comprising a different material.

While membrane 700 is shown to substantially cover the entire front face708 of the cassette body 702 in FIG. 7, in alternate embodiments, themembrane 700 can cover only a portion of the front face 708 of cassettebody 702. For example, in some embodiments, the membrane 700 can besized such that it extends from the proximal end 716 of the cassettebody 702 towards the distal end 718 of the cassette body 702, but doesnot reach the distal end 718. The membrane 700 can be sized such that itdoes not extend substantially further than the distal end 720 of thewindows 704. The membrane can be configured such that it restssubstantially entirely on the front face 708 of the cassette body 702.In alternate embodiments, at least a portion of the membrane 700 can bein contact with and/or secured to one or more of the cassette body sides710, 712.

One or more membranes 700 can be removably or permanently attached orcoupled to any portion of a cassette 702 in any suitable fashion. Forexample, a membrane 700 can be secured to a cassette body 702 such as bya tape or other adhesive. In other embodiments, one or more membranes700 can be fixed to a cassette body 702 with screws, clamps, thermalbonding, electrostatic force, or any appropriate method. Membranes 700can be used to keep the sample physically separate from the electrodesin the buffer pool outside the cassette body, thus substantiallyavoiding degradation of the biomolecule of interest, which can occur ifthe sample directly contacts or comes very close to the electrode.

Membranes 700 can comprise any material suitable for the particularapplication. In some embodiments, membrane 700 can be semi-permeable,allowing a buffer solution to pass through the membrane 700 and into theupper chamber 706, but not allowing other compounds, such asbiomolecules of interest, to pass through the membrane 700 into thebuffer solution outside of the upper chamber 706. For example, in someembodiments, membrane 700 can comprise a semi-permeable membrane havinga molecular weight threshold that allows small molecules to pass throughwhile retaining larger molecules, such as free biomolecules orbiomolecules of interest. The molecular weight threshold can be fromabout 1 kilodalton (kDa) to about 300 kDa or greater. Suitable membranematerials include, by way of example, dialysis filtration material, suchas regenerated cellulose, cellophane, or cellulose ester.

In addition to or instead of a membrane, some embodiments of anelectrophoresis device according to the present disclosure can includean electrode insert, such as electrode insert 1100, shown in FIGS.11-12. Electrode insert 1100 can include one or more extensions 1102,1104, that can position a wire 1106. Screws 1108 can serve as electrodeterminals and/or can secure wire 1106 to the electrode insert 1100. Theembodiment shown in FIGS. 11-12 includes two extensions 1102, 1104.Other embodiments, however, can include more or fewer than twoextensions. In the illustrated embodiment, wire 1106 enters a via 1110near a first side 1112 of the electrode insert 1100. Via 1110 can allowthe wire 1106 to pass from the proximal end 1114 of the electrode insert1100 to an intermediary surface 1116, and further around a firstextension 1102, such that the wire 1106 passes through grooves 1120provided in the first extension 1102 near the distal end 1118 of theelectrode insert 1100. The wire 1106 can then pass through a second via1122, returning to the proximal end 1114 of the electrode insert, andcan continue through a third via 1124, through grooves 1120 of secondextension 1104, and finally through a fourth via 1126, thus exiting theelectrode insert 1100 at the proximal end 1114, secured with a screw1108 near the second side 1128 of the electrode insert 1100.

The wire 1106 of electrode insert 1100 can be electrically coupled to asource of electricity (e.g., current), such as a battery or powersource. In some embodiments, the wire 1106 can be connected to apositive terminal at one side of the electrode insert 1100, andconnected to ground or a negative terminal at the opposite side of theelectrode insert 1100. The polarity of such electrical connections canbe reversible. Electrode inserts 1100 can be molded or machined ofmaterials such as those described for use with the cassette body.Electrode inserts can be shaped to interconnect or mate with disclosedcassette bodies such that, for example, extensions 1102, 1104 projectinto the upper chambers of a cassette body, and the intermediary surface1116 rests on or in the shelf or proximal end of the cassette body.

Wire 1106 can comprise any suitable conductive material. For example,wire 1106 can comprise any metal or metal alloy. In some embodiments,wire 1106 can be coated so as to substantially prevent a buffer solutioncontaining a sample from coming into direct contact with the electrode.For example, the electrode can be coated with platinum, titanium,tantalum, Nafion, and/or combinations thereof.

FIGS. 14-19 illustrate another embodiment of an electrophoresis cassettebody 1400 according to the present disclosure. As shown in FIGS. 8-10and described below, cassette body 1400 can be used in conjunction withone or more buffer baths in order to perform various methods ofperforming gel electrophoresis. The use of a membrane with the cassettebody 1400 can allow for physical separation between the sample and theelectrode, thereby preventing degradation of the sample that can resultfrom contact with the electrode.

Cassette body 1400 can include one or more chambers or channels 1402(best seen in FIGS. 16 and 18) from a proximal opening 1412 at or near aproximal end 1408 of the cassette body 1400 to a distal opening 1414 ator near a distal end 1410 of the cassette body 1400. The chambers 1402further include a window 1416, which results in an upper portion 1404 ofthe chamber 1402 being open to the space external to cassette body 1400.For example, the windows 1416 allow for fluid communication between thechambers 1402 and a buffer solution adjacent the front face 1422 of thecassette body.

Opposite the front face 1422, a rear face 1424 can include boredportions 1418 adjacent the distal end 1410 of the cassette body 1400.Such bored portions 1418 can allow for fluid flow around the entireperiphery of a lower portion 1432 of the chambers 1402. In someembodiments, the bored portions 1418 can allow for better thermalconditions, such as keeping the contents inside the chambers 1402 coolerthan would be the case if fluid flow was not permitted around the entireperiphery of the lower portion 1432 of chamber 1402.

Chambers 1402 are shown as substantially cylindrical or tubular chambers1402, but other configurations are also possible. For example, chambershaving substantially oval, square, rectangular, triangular, or othershaped cross-sections are possible.

As best shown in FIGS. 14 and 16, one or more combs 1440 and caps 1420can optionally be used with cassette body 1400 to form a gel withinchamber 1402. Comb 1440 can include a stopper portion 1442, an elongateportion 1444, and a projection 1446. Comb 1440 can be shaped to engagewith cassette body 1400. For example, the stopper portion 1442 can bepositioned such that at least a portion of surface 1450 of the comb 1440rests on a recessed surface 1406 and/or a raised surface 1448 of thecassette body 1400. In this configuration, the elongate portion 1444 andthe projection 1446 can be positioned within the chamber 1402. In theembodiment shown, the diameter of the elongate portion 1444 issubstantially the same as the volume, or size, of the chamber 1402. Thevolume of the projection 1446 is substantially smaller than the volumeof the chamber 1402 and generally can correspond to a sample volume tobe electrophoresed in the cassette. Other arrangements are alsopossible.

A cap 1420 with a seal near the distal end 1430 of the cap 1420 can bepositioned such that the cap 1420 closes off the distal openings 1414 ofthe chambers 1402. In preparation for running an electrophoresis gelusing the cassette body 1400, a compound such as agarose orpolyacrylamide can be introduced into the chambers 1402. One or morecombs 1440 can then be positioned within the chambers 1402 such that theprojections 1446 displace a volume of the compound equal to the volumeof the projection 1446. Once the compound becomes a gel, the combs 1440and cap 1420 can be removed from the cassette 1400. As shown in FIG. 18,a cross-linked gel 1426 can thus be formed in the chambers 1402, havingan indentation 1428 in the upper portion formed by projection 1446wherein a sample can be loaded. After removal of the cap 1420, thedistal opening 1414 of the chamber 1402 can be in fluid communicationwith a buffer bath for electrophoresis. Alternatively, a pre-made gelcan be inserted into chamber 1402, in which case combs 1440 and caps1420 would not be used.

As best seen in FIGS. 17-18, one or more membranes 1452 can be coupledto the cassette body 1400. Membranes 1452 can be used to keep a samplephysically separate from the electrodes in the buffer pool outside thecassette body, thus substantially avoiding degradation of thebiomolecule of interest, which can occur if the sample directly contactsor comes very close to the electrode. In some embodiments, one or moremembranes 1452 can cover at least a portion of at least one window 1416provided in a chamber 1402. In other embodiments, one or more membranes1452 can substantially cover the entire window 1416 of each chamber1402. Alternatively, as shown in the illustrated embodiment, a separatemembrane 1452 can be provided for each window 1416 and desirably issized to over the entire window. In some embodiments with a plurality ofmembranes 1452, each membrane 1452 can be substantially the samethickness, and can comprise the same material. In other embodiments witha plurality of membranes 1452, one or more membranes 1452 can bedifferent from one or more other membranes 1452, such as by being adifferent thickness and/or comprising a different material.

One or more membranes 1452 can be removably or permanently attached orcoupled to any portion of a cassette 1400 in any suitable fashion. Forexample, a membrane 1452 can be secured to a cassette body 1400 such asby tape or other adhesive. In other embodiments, one or more membranes1452 can be fixed to a cassette body 1400 with screws, clamps, thermalbonding, electrostatic force, or any appropriate method.

A seal 1454, such as a silicone seal, can be positioned adjacent themembrane 1452 so as to prevent leakage around the membrane 1452. Forexample, in the specific embodiment shown, a recess 1456 can be providedin the front face 1422 of the cassette body 1400 adjacent each window1416. A membrane 1452 can be positioned in each recess 1456 such that itcompletely covers the window 1416. A seal 1454 (e.g., a thin siliconerubber seal) can be positioned between the membrane 1452 and the window1416, as shown in FIGS. 17-18. The seal 1454 can be secured in thecassette body in any suitable fashion. Solely by way of example, in oneembodiment the seal 1454 can be retained with a seal cap 1458. The sealcap 1458 can be held in place by welding or bonding it to the cassettebody or by using a removable retaining clip 1460 if necessary.

Membranes 1452 can comprise any material suitable for the particularapplication. In some embodiments, membrane 1452 can be semi-permeable,allowing a buffer solution to pass through the membrane 1452 and intothe chamber 1402, but not allowing other compounds, such as biomoleculesof interest, to pass through the membrane 1452 into the buffer solutionoutside of the chamber 1402. For example, in some embodiments, membrane1452 can comprise a semi-permeable membrane having a molecular weightthreshold that allows small molecules to pass through while retaininglarger molecules, such as free biomolecules or biomolecules of interest.The molecular weight threshold can be from about 1 kilodalton (kDa) toabout 300 kDa or greater. Suitable membrane materials include, by way ofexample, dialysis filtration material, such as regenerated cellulose,cellophane, or cellulose ester.

Embodiments of cassette bodies can be machined, shaped, or molded toengage with one or more other components to form an electrophoresisapparatus. For example, a cassette body can be provided with fasteners,raised lips, shelves, raised bumps or depressions in order to securelyengage a buffer bath. Some embodiments of cassette bodies can be moldedor otherwise formed such that a plurality of cassette bodies can bestacked against or on top of one another. Cassette bodies can be usedalone or in conjunction with one or more other cassette bodies in anoverall electrophoresis device.

While the device shown in FIGS. 1-4 comprises two upper chambers 102 andtwo lower chambers 104 and the device shown in FIGS. 14-18 comprises twochambers 1402, other embodiments of suitable cassette bodies can containmore or fewer chambers, each of which can receive a separate gel toperform electrophoresis on a separate sample. For example, alternateembodiments of a cassette body can contain only one chamber (or oneupper chamber and one lower chamber). Similarly, other embodiments ofcassette bodies can contain three or more chambers. Cassette bodies canbe configured for vertical and/or horizontal electrophoresis.

Cassette bodies can be constructed from a variety of materials, such asglasses and plastics, such as, for example, acrylic, polycarbonates,polystyrenes, polymethyl methacrylate, polyethylene polyfluoroethylene,polypropylene polyurethane, polyethylene terephthalate,polytetrafluoroethylene and the like. In some embodiments, a cassettebody can be molded or machined or otherwise formed from a resin or hardplastic, as appropriate for particular applications. Whereasconventional electrophoresis devices comprises two parallel glassplates, cassette bodies according to the present disclosure can comprisea unitary or monolithic glass or plastic body, for example a machinedacrylic body, which can provide advantages such as manufacturing easeand can also allow for easy movement of the cassette body, such as fromone buffer bath to another.

Cassette bodies can be combined with an electricity source and one ormore buffer baths in order to provide an electrophoresis apparatus.Cassette bodies and electrophoresis apparatus according to the presentdisclosure can be used in methods of running electrophoresis gels, to,for example, separate and purify a biomolecule of interest.

B. Methods

Embodiments of a method of performing an electrophoresis gel operationare illustrated schematically in FIGS. 8-10 and in a block diagram inFIG. 13. A cassette body 800 (which is a schematic representation ofcassette body 100 or cassette body 1440) can comprise an upper chamberportion 802 with a window opening covered by a semi-permeable membrane804. Semi-permeable membrane 804 can separate the upper chamber portion802 from a first buffer solution 806 contained in a first container 808.Cassette body 800 can also comprise a lower chamber portion 810,containing a cross-linked native page gel 812 having a sample 814 loadedon top of the gel 812 (e.g., in an indentation at the proximal end ofthe gel), adjacent the upper chamber portion 802. The gel 812 in thelower chamber portion 810 can be in fluid contact with a second buffersolution 816 contained in a second buffer container 818, such as via asmall opening in the bottom of the container 808 adjacent the lowerchamber portion 810. The second buffer solution 816 is in fluid contactwith the gel 812 but is otherwise separated from the contents of thecontainer 808, including the first buffer solution 806.

An electrical circuit can connect the first buffer solution 806 and thesecond buffer solution 816 via electrodes 828, 830 (e.g., wires)submerged in the solutions 806, 816. For example, a negative charge canbe applied to the first buffer solution 806, and a positive charge canbe applied to the second buffer solution 816. Such charges can beapplied for a period of time sufficient to separate any free probes 820in the sample 814 from any biomolecules of interest 822, such asDNA/protein complex 822. For example, charges can be applied for aboutthirty minutes. During such time, as shown in FIG. 9, free probes 820can elute out of a distal opening of the lower chamber portion 810 andmigrate into the second buffer solution 816, while the DNA/proteincomplex 822 can remain within gel 812 contained in the lower chamberportion 810 of the cassette body 800.

After the free probes 820 have been separated out, the second buffersolution 816 containing those free probes 820 can be discarded. Forexample, the second buffer container 818 can be drained of the secondbuffer solution 816, and a new buffer solution can be added to thesecond buffer container 818. In alternative embodiments, the cassettebody 800 and first buffer container 808 can be removed from theirconnection with the second buffer container 818, and placed inconnection with a new buffer container containing a new buffer solution.In other embodiments, the second buffer solution need not be discardedand can be reused when the current is reversed, as described below.

FIG. 10 illustrates a fresh buffer solution 824, contained in a newbuffer container 826. Once the cassette body 800 is arranged such thatthe first buffer solution 806 is in fluid contact with thesemi-permeable membrane 804 and the lower chamber portion 810 is influid contact with the fresh buffer solution 824, the polarity of thecharges can be reversed. For example, a positive charge can be appliedto the first buffer solution, and a negative charge can be applied tothe fresh buffer solution 824 for a period of time sufficient for theDNA/protein complex 822 to migrate up from the lower chamber portion810, out of the gel and into the upper chamber portion 802 (e.g., theDNA protein/complex 822 can migrate towards the proximal end of thecassette body 800). For example, a reverse current can be applied foraround forty minutes. A controller 840 (FIG. 8) can be used toautomatically control the current polarity. For example, a controller840 can be programmed to apply a current in one direction for a firstpredetermined period of time, and then to apply a current in theopposite direction for a second predetermined period of time. Similarly,the controller 840 can be programmed to switch the current polarity atprescribed intervals, as desired by the user. Controller 840 caninclude, for example, a processor, a display, and one or more controlswitches for varying parameters.

As shown in FIG. 10, the DNA/protein complex 822 can be contained withinsome of the buffer solution 806 within the upper chamber 802 of thecassette body 800, substantially without passing through thesemi-permeable membrane 804. In some embodiments, buffer solution 806can pass freely through membrane 804, while the biomolecule of interest822 substantially cannot pass through the membrane 804. Thus, theDNA/protein complex 822 can be contained within the relatively smallvolume of the upper chamber portion 802, as opposed to in the largevolume of one of the buffer pools. This can allow for easier collectionof and simultaneous concentration of a biomolecule of interest, whencompared to conventional methods of performing electrophoresis. Forexample, instead of having to remove a parallel glass plates and sliceinto the cross-linked gel to gain access to the biomolecule of interest,as is required with typical conventional electrophoresis devices, withembodiments of the present cassette body and electrophoresis device, thebiomolecule of interest can simply be contained in a small volume ofbuffer solution in the upper chamber This location of the DNA/proteincomplex 822 can also allow of the cassette body (e.g., easily accessiblenear the proximal end of the cassette body). In this way, thebiomolecule of interest can be collected in a simple way, such as bywithdrawing about 500 microliters of solution from the upper chamber ofthe cassette body via openings along the upper edge of the cassettebody, such as by using a micropipette.

Buffer solutions 806, 816, and 824 can be any solution that supportselectrophoresis. In some embodiments, solutions 806, 816, and/or 824 canbe a salt solution. In some embodiments, solutions 806, 816, and/or 824can be a buffer solution. Examples of salt solutions include: NaCl, KCland the like. Examples of buffer solutions include: Tris, HEPES, MOPS,PBS, EDTA, Tris Buffered Saline, Tris-Borate-EDTA (TBE), TAE, TGE,glycerol, glycine and the like, and mixtures thereof. In certainembodiments, the first buffer solution 806 (referred to as thecollection buffer solution) comprises glycerol, Tris, glycine and EDTA.In a specific implementation, the first buffer solution 806 comprises 5%glycerol (by volume), 0.75M Tris pH 8.4, 38 mM glycine, and 2 mM EDTA.

While the embodiments shown in FIGS. 8-10 show a cassette body having amembrane covering an opening to the upper chamber portion, otherembodiments can comprise an electrode insert that submerges at least aportion of a wire into the upper chamber of the cassette body, inaddition to or instead of membrane 804. Exemplary electrode inserts aredescribed above.

FIG. 13 illustrates a block diagram of one method of performing anelectrophoresis operation using the electrophoresis devices and cassettebodies according to the present disclosure. The methods can include,loading a sample that includes the free biomolecules and the complexesthat include the biomolecules of interest (which can include adetectable label) to the proximal end of the electrophoresis gel, forexample in a cassette body arranged in buffer solutions, as describedabove (step 1300). The sample can be electrophoresed for a period oftime sufficient for the free biomolecules to elute from the distal endof the electrophoresis gel, such that the period of time is not longenough so that the complexes including the biomolecules of interestelute from the distal end of electrophoresis gel and are thereforeretained in the electrophoresis gel (step 1302). In this way, thecomplexes including the biomolecules of interest can be separated fromthe free biomolecules. The time required for the free biomolecules topass through the gel is dependent upon such factors as applied current,buffer conditions, gel concentration and gel length and the physicalcharacteristics of the biomolecules. The free biomolecules can bediscarded, for example by letting them elute from the distal end of thegel into surrounding buffer, or they can be collected, for example usinga collector attached to the end of the gel, such as a collector with asemi-permeable membrane that allows buffer through, but retains the freebiomolecules (step 1304).

Once the buffer solution containing the free biomolecules has beenremoved, a clean buffer solution can be provided (step 1306) to replacethe buffer solution containing the free biomolecules. Removing thebuffer solution contaminated with free biomolecules can substantiallyprevent the free biomolecules from migrating back up into the gel andupper chamber of the cassette when the current is reversed. Thus, anisolated biomolecule of interest can be collected. However, inalternative embodiments, the buffer solution need not be discarded orreplaced. To collect the complexes containing the biomolecules ofinterest, the current can be reversed relative to the electrophoresisgel, and the biomolecules remaining in the gel can reverse theirdirection of travel relative to the electrophoresis gel (step 1308).

Reversing the current relative to the electrophoresis gel can be done byreversing the polarity of an electrophoresis apparatus, for example byreversing the direction of the current, while the gel is kept in thesame position with respect to the electrophoresis apparatus. Inalternative embodiments, the orientation of the gel can be reversed withrespect to the applied electric current, without reversing the directionof the current. The gel can then electrophoresed for a second period oftime sufficient for the complexes of bound biomolecules of interest toelute from the proximal end of the electrophoresis gel (step 1310). Thebiomolecules of interest can then be collected, for example using acollector attached to the end of the gel, such as a collector with asemi-permeable membrane that allows buffer through, but retains thebiomolecules of interest (step 1312). In some embodiments, the collectorcan be an integral part of the cassette, as described above, or aseparate component mounted on the gel. In some embodiments, thebiomolecules of interest can be collected, such as with a micropipette,from the upper chamber of the cassette body.

Any biomolecule of interest can be purified using the disclosed methods.For example the methods disclosed herein can be used to purify nucleicacids of interest or polypeptides of interest. Thus, in some examples abiomolecule of interest is a polypeptide, such as a peptide or protein,for example a receptor, a receptor ligand, an antibody, an antigen, asoluble protein, or an insoluble protein and the like. In some examplespolypeptides of interest include one or more antibodies. In someembodiments, polypeptides of interest include one or more antigens. Insome examples, the biomolecules of interest are nucleic acid molecules,such as DNA, RNA or combinations thereof.

In some embodiments, the biomolecule of interest is a nucleic acid thatis double stranded, single stranded, or a combination thereof. In someembodiments, the biomolecules of interest are partially double-strandednucleic acid probes, such as those described in International PatentPublication WO 2008/147899, which is incorporated herein by reference inits entirety. International Patent Publication WO 2008/147899 claims thebenefit of U.S. Provisional Application No. 60/939,826 which is alsoincorporated herein by reference in its entirety. Further details,including suitable gel materials, suitable membrane materials, andsuitable buffer solution materials can be found in PCT ApplicationPCT/US09/35689, which is hereby incorporated herein by reference in itsentirety.

An application of the disclosed methods is the rapid and efficientdetermination of the sequence binding requirements for a givendouble-stranded nucleic acid binding protein, such as a double-strandedDNA binding protein, for example a transcription factor, such as anactivated transcription factor. For example, by constructing a libraryof different double-stranded sequences and determining which sequences aparticular transcription factor binds to it, it is possible to rapidlyidentify the sequence requirements for a given transcription factor in ahigh throughput manner. Using the disclosed methods, suchdouble-stranded sequences bound by transcription factors can be rapidlypurified from unbound double-stranded sequences.

In some examples, a partially double-stranded nucleic acid probeincludes two portions, a double-stranded portion and a single-strandedportion. The single-stranded portion includes a nucleotide sequencecorresponding to an index sequence, such as but not limited to the indexsequences described in International Patent Publication WO 2008/147899,which is incorporated herein by reference in its entirety. InternationalPatent Publication WO 2008/147899 claims the benefit of U.S. ProvisionalApplication No. 60/939,826, which is also incorporated herein byreference in its entirety.

The second portion of a partially double-stranded nucleic acid probe isa double-stranded portion selected such that it contains one or morepotential binding sites for double-stranded nucleic acid bindingproteins, such as transcription factors. For example, a partiallydouble-stranded nucleic acid probe can contain 1, 2, 3, 4, 5, 6, 7, 8,9, 10, or even more potential binding sites for double-stranded nucleicacid binding proteins, such as transcription factors, for exampleactivated transcription factors. The double-stranded portion of thedisclosed partially double-stranded nucleic acid probes are typicallygreater than about 8 nucleotide base pairs in length such as greaterthan about 8, about 9, about 10, about 11, about 12, about 13, about 14,about 15, about 20, about 25, about 30, about 35, about 40, about 45,about 50, about 60, about 70, about 80, about 90, about 100, about 120,about 140, about 160, about 180, about 200, about 250, about 300, oreven greater than about 350 base pairs in length such as 8-50nucleotides, 8-100 nucleotides, 8-200 nucleotides, 8-300 nucleotides,8-500 nucleotides, or even greater than 500 nucleotides in length.

For the detection and/or isolation of biomolecules of interest,biomolecules of interest can include a label. The binding partner(s) ofbiomolecules of interest can include a label. Thus, in some embodiments,the biomolecules of interest and/or their binding partners aredetectably labeled, with any isotopic or non-isotopic label known in theart. Non-isotopic labels can, for instance, include a fluorescent orluminescent molecule, biotin, an enzyme or enzyme substrate or achemical. Isotopic labels can, for instance, include ³⁵S ¹⁴C, ³²P, ¹²⁵I,³H isotopes and the like. Methods for labeling and guidance in thechoice of labels appropriate for various purposes are discussed forexample in Sambrook et al. (Molecular Cloning: A Laboratory Manual, ColdSpring Harbor, N.Y., 1989) and Ausubel et al. (In Current Protocols inMolecular Biology, John Wiley & Sons, New York, 1998).

The methods described above are depicted schematically in FIGS. 8-10.Again with reference to FIG. 8, a sample 814 is applied to a proximalend 832 of the electrophoresis gel 812. With reference to FIG. 9, ascurrent is applied by the application of an electric field toelectrophoresis gel 812, the biological macromolecules (such as the freebiomolecules and complexes containing biomolecules of interest) areseparated by the distance traveled through the gel as a function of time(the direction of migration is indicated by arrow 836). Still withreference to FIG. 9, (in which the free biomolecules have a lowermolecular weight) the free biomolecules will travel further as afunction of time compared to molecular complexes that contain abiomolecule of interest because the molecular complexes have largermolecular weights.

The sample 814 that included the free biomolecules 820 and molecularcomplexes 822 is electrophoresed for a period of time sufficient for thefree biomolecules 820 to elute off distal end 834 of electrophoresis gel812 into the buffer solution 816. The period of time is not long enoughso that the complexes including the biomolecules of interest 822 elutefrom distal end 834 of electrophoresis gel 812, but rather thebiomolecules of interest 822 are retained in electrophoresis gel 812.The free biomolecules 820 can be discarded, for example by letting themflow into the surrounding buffer 816, or they can be collected, forexample using a collector, which can contain a semi-permeable membranewith a molecular weight threshold that allows the buffer to pass throughbut retains the free biomolecule 820 (exemplary semi-permeable membranesare described above).

With reference to FIG. 10, the direction of electrophoresis issubsequently reversed, for example by reversing the polarity ofelectrodes 828, 830. The biomolecules of interest 822 then travel in adirection opposite to the direction in which they originally traveled(as indicated by arrow 838). Electrophoresis is continued for a periodof time sufficient for the complexes of bound biomolecules of interest822 to elute from proximal end 832 of the electrophoresis gel 812. Themolecular complexes of bound biomolecules of interest 822 can becollected, for example using a collector, which can containsemi-permeable membrane with a molecular weight threshold that allowsthe buffer 806 to pass through but retains the molecular complexes 822(exemplary semi-permeable membranes are described above). In otherembodiments, the biomolecules of interest can be collected from theupper chamber 802, such as with a micropipette.

Biomolecules of interest and isolated molecular complexes can becollected and used for any purpose, for example for further analysis. Insome examples, the biomolecules of interest are nucleic acid molecules,for example nucleic acid molecules to which transcription factors havebound. Thus, the methods can be used to separate nucleic acid moleculesto which transcription factors have bound from nucleic acid moleculesthat have not been bound by transcription factors. The complexescontaining such transcription factors can be collected and analyzed, forexample using the methods described in International Patent PublicationWO 2008/147899, which is incorporated herein by reference in itsentirety. International Patent Publication WO 2008/147899 claims thebenefit of U.S. Provisional Application No. 60/939,826 which is alsoincorporated herein by reference in its entirety. In other examples, themethods disclosed herein are used to separate protein complexes fromfree protein, for example a complex of antigen and antibody from freeantigen or conversely from free antibody.

Cassette bodies according to the present disclosure can thus be used inmethods of performing electrophoresis to separate and/or purifybiomolecules of interest from a sample, while avoiding contact betweenthe electrode and the sample, thus substantially avoiding the risk ofdamaging or denaturing the biomolecule of interest.

C. Electrophoresis Gels

The methods and devices disclosed herein involve the use of anelectrophoresis gel for the separation and/or purification ofbiomolecules of interest, such as biomolecules of interest in amolecular complex. Electrophoresis gels suitable for the disclosedmethods include gels composed of one or more polysaccharides (such asagarose), crossed linked polymers (a combination of cross-linkablemonomers, for example acrylamide, that can be polymerized by across-linker, for example N,N′-methylenebisacrylamide) and combinationsthereof.

The electrophoresis gels for use in the disclosed methods can be madefrom at least one polysaccharide, such as at least 1, at least 2, atleast 3, at least 4, or more polysaccharides. In some embodiments, thepolysaccharide is agarose or an agarose derivative, such as an agarosederivative which contains hydroxyethyl groups (for example, thosedisclosed in U.S. Pat. Nos. 3,956,273 and 4,319,975, or available from acommercial source, such as SEAKEM®, or NUSIEVE®), and the like. In otherembodiments, the polysaccharide is cellulose or a cellulose derivative,such as hydroxyethyl cellulose, hydroxypropylmethyl, cellulose methylcellulose, or the like. Agarose and cellulose are similar in that theyare both linear polymers. They differ in their sugar constituents, inglycosidic linkages, and in the ability to form gels. While derivatizedcelluloses remain in solution at high and low temperatures, agarosepolymers form thermally reversible gels. In other embodiments, thepolysaccharide is galactomannan, dextran, starch, levan, glucan, mannan,xylan, or other polysaccharide. In specific embodiments, thepolysaccharide is agarose, a derivative thereof, or a combinationthereof.

Electrophoresis gels useful for the disclosed methods typically containfrom about 0.1% polysaccharide to about 7% polysaccharide, such as about0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about0.7%, about 0.8%, about 0.9%, about 1.0%, about 1.1%, about 1.2%, about1.3%, about 1.4%, about 1.5%, about 1.6%, about 1.7%, about 1.8%, about1.9%, about 2.0%, about 2.1%, about 2.2%, about 2.3%, about 2.4%, about2.5%, about 2.6%, about 2.7%, about 2.8%, about 2.9%, about 3.0%, about3.0%, about 3.1%, about 3.2%, about 3.3%, about 3.4%, about 3.5%, about3.6%, about 3.7%, about 3.8%, about 3.9%, about 4.0%, about 4.1%, about4.2%, about 4.3%, about 4.4%, about 4.5%, about 4.6%, about 4.7%, about4.8%, about 4.9%, about 5.0% about 5.1%, about 5.2%, about 5.3%, about5.4%, about 5.5%, about 5.6%, about 5.7%, about 5.8%, about 5.9%, about6.0% about 6.1%, about 6.2%, about 6.3%, about 6.5%, about 6.5%, about6.6%, about 6.7%, about 6.8%, about 6.9%, or about 7.0% polysaccharide.The choice of percentage can be made based on factors such as theresolution required and the polysaccharide selected.

The electrophoresis gels made from cross-linked polymers for use in thedisclosed methods can include the reaction mixture from the free radicalpolymerization reaction product of a mixture of at least one monomer,such as at least 1, at least 2, at least 3, at least 4, or moremonomers, and at least one cross-linker, such as at least 1, at least 2,at least 3, at least 4 or more cross-linkers sufficient to cross-linkthe monomer. Suitable cross-linkable monomers include acrylamide,acrylamide derivatives (such as N-methylacrylamide,N,N-dimethylacrylamide, N-(hydroxymethyl)acrylamide, diacetonacrylamide,N-hydroxypropylacrylamide, and those disclosed in U.S. Pat. No.5,185,466), other monomers, such as those disclosed in U.S. Pat. No.5,840,877 (for example N-acryloyl-tris(hydroxymethyl)aminomethane, orN-acryloyl-1-amino-1-deoxy-D-galactitol), or a combination thereof.Other monomers that can be used in the disclosed methods include theacrylic monomers based on sugar alcohols disclosed in U.S. Pat. Nos.5,185,466 and 5,202,007 and those disclosed in U.S. Pat. No. 5,319,046.It is contemplated that any of the monomers described herein can be usedin the disclosed methods in any combination such that the resultantpolymer gel is capable of separating biomolecules. In some embodiments,the monomer is acrylamide, N-methylacrylamide, N,N-dimethylacrylamide,N-(hydroxymethyl)acrylamide, diacetonacrylamide,N-hydroxypropylacrylamide, N-acryloyl-tris(hydroxymethyl)aminomethane,N-acryloyl-1-amino-1-deoxy-D-galactitol, or a combination thereof. Inspecific embodiments, the monomer is acrylamide. A cross-linking agent,such those described in Gelfi and Righetti Electrophoresis 2:213-219,1981, or known to those of skill in the art can be used to form thecrosslinked polymer gels for use in the disclosed methods. Crosslinkedpolymer gels suitable for the disclosed methods contain a cross-linkercapable of cross-linking the monomers described herein. In someembodiments, the cross-linker is N,N′-methylenebisacrylamide,N,N′-propylenebisacrylamide, diacrylamide dimethylether,1,2-diacrylamide ethyleneglycol, ethylenureabisacrylamide, ethylenediacrylate, N,N′-diallyltartardiamide, N,N′-bisacrylylcystamine,N,N′-1,2-dihydroxyethylene-bisacrylamide, N,N-bisacrylyl cystamine,trisacryloyl-hexahydrotriazine, dihydroxyethylene-bis-acrylamide,piperazine-di-acrylamide, or a combination thereof. In certainembodiments, the cross-linker is N,N′-methylenebisacrylamide (BIS).Cross linking agents are typically used in an amount of about 2% toabout 30% by weight and preferably about 3% to about 15% by weight,based on the total weight of the monomer (such as acrylamide) and thecross-linking agent. Higher percentages of cross-linker typically resultin gels that increase in opacity as the percentage of cross-linkerincreases.

In some examples, cross-linked polymer electrophoresis gels useful forthe disclosed methods contain from about 0.1% cross-linked monomer toabout 15% cross-linked monomer, such as about 0.1%, about 0.5%, about1.0%, about 1.5%, about 2.0%, about 2.5%, about 3.0%, 3.5%, about 4.0%,about 4.5%, about 5.0%, about 6.0%, about 7.0%, about 7.5%, about 8.0%,about 8.5%, about 9.0%, about 9.5%, about 10.0%, 10.5%, about 11.0%,about 11.5%, about 12.0%, about 12.5%, about 13.0%, 13.5%, about 14.0%,about 14.5%, or about 15.0 cross-linked monomer. The choice ofpercentage can be made based on factors such as the resolution requiredand the monomer selected. For example, a percentage of monomer is chosenthat is capable if resolving a biomolecule of interest from freebiomolecules.

The cross-linking polymerization can be initiated in the presence of aperoxide and/or under irradiation of ultra-violet rays. The reaction canbe further accelerated by heat and irradiation with ultra-violet rays.As the polymerization catalyst, a known low temperature-polymerizationinitiator can be used, such as those described in Gelfi and RighettiElectrophoresis 2:213-219, 1981, Gelfi and Righetti Electrophoresis2:220-228, 1981; and Modern Electrophoresis edited by Aoki and Nagai(Hirokawa Shoten, 1973). Examples of initiators include a mixture ofbeta-dimethylaminopropionitrile and ammonium peroxodisulfate, a mixtureof N,N,N′,N′-tetramethylethylenediamine (TEMED) and ammoniumperoxodisulfate, a mixture of TEMED and riboflavin, a combination of amixture of TEMED, riboflavin and hydrogen peroxide, and irradiation withultra-violet rays. The most common system of catalytic initiationinvolves the production of free oxygen radicals by ammonium persulfate(APS) in the presence of the tertiary aliphatic amine TEMED.

The gel-based electrophoretic embodiments of this disclosure can becarried out in any suitable format, for example in standard-sized gels,tubes, minigels, strips, capillaries, and gels designed for use withmicrotiter plates and other high throughput (HTS) applications, and thelike. Formats for gels include those described in U.S. Pat. Nos.5,578,180; 5,922,185; 6,057,106; 6,059,948; 6,096,182; 6,143,154;6,162,338; 6,562,213, U.S. Patent Publications 20020134680, 20030127330and 20030121784; and published PCT Application Nos. WO 95/27197, WO99/37813, WO 02/18901 and WO 02/071024.

D. Samples

Appropriate samples for use in the methods disclosed herein include anyconventional biological sample for which separation and/or purificationof biomolecules of interest is desired. In some examples, samples can besamples of purified biomolecules, for example biomolecules recombinantlyor synthetically produced or purified from a biological source such asan organism. In some examples, samples include those obtained from,excreted by or secreted by any living organism (whether the organism islive or dead), such as a prokaryotic organism or a eukaryotic organismincluding without limitation, multicellular organisms (such as plantsand animals, including samples from a healthy or apparently healthyhuman subject or a human patient affected by a condition or disease tobe diagnosed or investigated, such as cancer), clinical samples obtainedfrom a human or veterinary subject, for instance blood orblood-fractions, biopsied tissue. Standard techniques for acquisition ofsuch samples are available. See, for example Schluger et al., J. Exp.Med. 176:1327-33 (1992); Bigby et al., Am. Rev. Respir. Dis. 133:515-18(1986); Kovacs et al., NEJM 318:589-93 (1988); and Ognibene et al., Am.Rev. Respir. Dis. 129:929-32 (1984).

Biological samples can be obtained from any organ or tissue (including abiopsy or autopsy specimen, such as a tumor biopsy) or can comprise acell (whether a primary cell or cultured cell) or medium conditioned byany cell, tissue or organ. In some embodiments, a biological sample is anuclear extract. Nuclear extract contains many of the proteins containedin the nucleus of a cell, and includes for example transcriptionfactors, such as activated transcription factors. Methods for obtaininga nuclear extract are well known in the art and can be found for examplein Dignam, Nucleic Acids Res, 11; 11(5):1475-89 1983.

In view of the many possible embodiments to which the principles of thedisclosed invention may be applied, it should be recognized that theillustrated embodiments are only preferred examples of the invention andshould not be taken as limiting the scope of the invention. Rather, thescope of the invention is defined by the following claims. We thereforeclaim as our invention all that comes within the scope and spirit ofthese claims.

We claim:
 1. A cassette for use with an electrophoresis device, comprising: a proximal end and a distal end opposite the proximal end; a front face and a back face; at least one chamber defined between the front face and the back face, the chamber having an upper portion and a lower portion, wherein the upper portion includes a proximal opening at or near the proximal end of the cassette and the lower portion includes a distal opening at or near the distal end of the cassette wherein the proximal opening and distal opening are aligned to form a straight passageway there through, and wherein the front face comprises at least one window opening into the upper portion of the chamber; and a semi-permeable membrane covering at least a portion of the at least one window opening.
 2. The cassette according to claim 1, wherein the semi-permeable membrane is removably secured to the front face of the cassette.
 3. The cassette according to claim 2, wherein the semi-permeable membrane is configured to allow buffer solution outside the cassette to pass through the membrane into the upper portion of the chamber, and to block passage of a biomolecule contained within the upper portion of the at least one chamber.
 4. The cassette according to claim 1, wherein the cassette comprises glass.
 5. The cassette according to claim 1, wherein the cassette comprises a unitary body.
 6. The cassette according to claim 1, wherein the inner surface of the chamber is substantially cylindrical.
 7. The cassette according to claim 1, further comprising a bored portion formed in the back face of the cassette, wherein the bored portion is configured to allow fluid flow around the entire periphery of at least a portion of the lower portion of the chamber, thereby separating the lower chamber from the cassette body facilitating cooling.
 8. An electrophoresis device, comprising: a first buffer container; and a cassette capable of being coupled to the first buffer container to form a first sidewall of the first buffer container, wherein the cassette comprises a proximal end and a distal end opposite the proximal end, a front face and a back face and at least one chamber defined between the front face and the back face, the chamber having an upper portion and a lower portion, wherein the upper portion includes a proximal opening at or near the proximal end of the cassette and the lower portion includes a distal opening at or near the distal end of the cassette wherein the proximal opening and distal opening are aligned to form a straight passageway there through, and wherein the front face comprises at least one window opening into the upper portion of the chamber.
 9. The electrophoresis device according to claim 8, wherein the cassette further comprises a semi-permeable membrane covering at least a portion of the window opening of the upper portion.
 10. A method of separating a biomolecule of interest from a sample, comprising: providing a sample, wherein the sample contains a biomolecule of interest and one or more biomolecules having a lower molecular weight than the biomolecule of interest; loading the sample onto a gel in a lower portion of a cassette body, wherein the cassette is coupled to a first buffer container to form a first sidewall of the first buffer container and comprises a proximal end and a distal end opposite the proximal end, a front face and a back face and at least one chamber defined between the front face and the back face, the chamber having an upper portion and a lower portion, wherein the upper portion includes a proximal opening at or near the proximal end of the cassette and the lower portion includes a distal opening at or near the distal end of the cassette wherein the proximal opening and distal opening are aligned to form a straight passageway there through; placing the first buffer container coupled to the cassette within a second buffer container; providing a buffer solution to both the first buffer container and the second buffer container; electrophoresing the sample by applying a current to the buffer in the first and second buffer containers for a time period sufficient for substantially all of one or more biomolecules having a lower molecular weight than the biomolecule of interest to elute out of the distal end of the lower portion of the cassette chamber, into the buffer solution in the second buffer container, leaving the biomolecule of interest within the gel; removing the buffer solution from the second buffer container; providing an additional amount of the buffer solution to the second buffer container to enable fluid contact with the lower portion of the cassette; reversing the current with respect to the gel; and electrophoresing the sample for a time period sufficient for substantially all of the biomolecule of interest to elute out of the proximal end of the lower portion, into the upper portion of the cassette chamber.
 11. The method according to claim 10, further comprising collecting biomolecule of interest.
 12. The method according to claim 11, wherein collecting the biomolecule of interest comprises withdrawing the buffer solution containing the biomolecule of interest from the upper portion of the cassette chamber.
 13. The method according to claim 11, wherein collecting the biomolecule of interest comprises securing a semi-permeable membrane over at least part of the upper portion, so as to prevent substantially all of the biomolecule of interest from passing through the semi-permeable membrane into the buffer solution in the first container in fluid contact with the upper portion of the cassette chamber.
 14. The method according to claim 13, wherein reversing the current with respect to the gel comprises switching the polarity of a first and second electrode in electrical contact with the buffer solution.
 15. The method according to claim 13, wherein reversing the current with respect to the gel comprises changing the orientation of the gel with respect to a first and second electrode in electrical contact with the buffer solution in the first buffer container and second buffer container.
 16. The method according to claim 10, wherein removing the buffer solution from the second buffer container comprises draining the buffer solution from the second buffer container, and wherein providing an additional amount of buffer solution to the second buffer container to enable fluid contact with the lower portion of the cassette comprises refilling the second buffer container with the additional buffer solution.
 17. The method according to claim 10, wherein removing the buffer solution from the second buffer container comprises removing the first buffer container coupled to the cassette from the second buffer container, and wherein providing an additional amount of buffer solution to the second buffer container to enable fluid contact with the lower portion of the cassette comprises placing the first buffer container coupled to the cassette in the second buffer container containing the additional buffer solution.
 18. The cassette of claim 1, wherein the proximal opening and the distal opening of the cassette consists of a single proximal opening and a single distal opening aligned to form a single straight vertical passageway there through.
 19. The cassette of claim 1, wherein the lower chamber is narrower than the upper chamber in the cassette.
 20. The cassette of claim 1, wherein the lower chamber further comprises a ridge at the bottom of the lower chamber.
 21. The electrophoresis device of claim 8, further comprising a second buffer container capable of holding buffer solution in fluid contact with the lower opening of the lower portion of the chamber of the cassette when the cassette is positioned in the first buffer container and the first buffer container is positioned within the second buffer container and at least one electrode.
 22. The electrophoresis device of claim 8, wherein the cassette further comprises a gel in the lower portion of the cassette. 